Installing Dependencies

The FlowCytometryTools is a python package. As such, it requires a python interpreter to work. In addition, this package makes use of a few scientific and data analysis libraries for python. All the dependencies are listed below, followed by a section containing instructions on how to install all the dependencies on the different operating systems.

Required Dependencies

  1. python : 2.6 or 2.7 (note that python 3.0 or higher are not yet supported!)
  2. pandas (Recommended version: 0.12.0 or higher).
  3. matplotlib: (Recommended version: 1.13.1 or higher).
  4. scipy

Optional Dependencies

  1. wx-python : Used for the FlowCytometryTools GUI.

Windows / MacOS users

A simple way of obtaining the dependencies is by installing either canopy or anaconda.

If you intend to use the GUI, you’ll still need to install wx-python.

Debian/Ubuntu users

You have at least two options:

  1. Installing using the command line (this is the better option if you’re comfortable with the command line).

    Open a terminal window and enter the following:

    sudo apt-get build-dep python-matplotlib  # Dependencies of matplotlib
sudo apt-get install python-pip python-dev
sudo apt-get install python-wxgtk2.8 # Optional dependency for FlowCytometryTools GUI
sudo pip install --upgrade pip
sudo pip install setuptools
sudo apt-get install gfortran libopenblas-dev liblapack-dev # Dependencies for scipy
sudo pip install pyzmq jinja2 tornado # Dependencies for ipython notebook
sudo pip install numpy scipy matplotlib ipython ipython-notebook pandas sympy

    This should install both optional and required the dependencies. Please shoot us an email if we forgot to include something. (Or if you have specific instructions for a different flavor of unix.)

  2. Alternatively, you can install a distribution like canopy or anaconda.

    Note

    canopy/anaconda may not come with wx-python. In this case, in order to use the GUI, you’ll still need to install wx-python. Also, after installing it make sure that canopy/anaconda know how to find your installation of wx-python.

Installing FlowCytometryTools

IMPORTANT Make sure all required dependencies are installed before you proceed to install the package!

Using git

This option is recommended if you intend to contribute to developing the FlowCytometryTools library.

  1. Install git on your machine. Please give git access to the command line. If you don’t, the git commands below won’t work.

  2. Open your command terminal

  3. In your command terminal enter:

    ipython -c 'import os, matplotlib; print os.path.split(matplotlib.__path__[0])[0];'

  4. The printed path will be your site-packages path!

  5. In the command terminal navigate to that path:

    cd (enter here the path you got above)

  6. Enter the commands below:

    git clone https://bitbucket.org/gorelab/goreutilities.git GoreUtilities
git clone https://bitbucket.org/gorelab/flowcytometrytools.git FlowCytometryTools
cd FlowCytometryTools
git checkout [version number]

Updating using git

If you’ve installed the package using git, you can also use git to update the package when new releases are available. To update:

cd (enter here the path you got above)

cd GoreUtilities
git fetch origin
git pull
git checkout [needed version/branch]

cd ..

cd FlowCytometryTools
git fetch origin
git pull
git checkout [needed version/branch]